False Life
by Cait98
Summary: Maggie finds herself in a spot of bother when Supergirl reveals a secret that could change their lives forever.
1. Chapter 1

"Danvers." Maggie said sternly as she walked into the main command centre of the DEO. Alex was standing with arms crossed looking at the projected image above. She passively nodded as she drummed her fingers on her arm, "Maggie." Alex said blankly.

Maggie looked up at the projected image, "Metallo?" She asked curiously, "I thought he was destroyed wayback."

"Me too, but it looks like CADMAS are one step ahead of us. We recently beat Daxamite butt, and now this..." She said rather calmly, clearly worried, "And Kara is off-radar, I j-Something is wrong with her Maggie and I don't know how to fix it. I know Mon-El left a few months ago and I thought she was over that with how happy she's seemed."

Maggie put her arms around Alex's shoulder and pulled her close. Alex felt her lip trembling slightly, "I'm trying, you know to see it from her point of view, if I were in her shoes but..."

"Grief takes many forms Danvers. She will have up days, down days and all of the inbetween." She said softly, before kissing her cheek, "Just give her time." Alex nodded, before hugging Maggie, keeping hold of her for a while longer than she should. She then frowned at the sight of Supergirl, "Supergirl?" Alex said with shock as she let go of Maggie. Maggie turned around, "Little Danvers, where have you been?"

"And wouldn't you like to know." Supergirl bit back in response. Maggie frowned, confused as to the way she was acting. She understood she was grieving, but like Alex, she thought she would be past the anger and blame stage by now.

Alex watched as Supergirl stood staring at the screen with her knuckles firmly placed on her hips. She approached her slowly, "Are you...Are you okay?" Alex asked softly.

"On top of the world Alex!" Kara snapped, sarcastically before catching sight of Maggie, and her glare was firmly fixed on Maggie. If looks could kill, this would be it. Kara rotated so her full front was facing Maggie, but she did not say anything. As Maggie was looking at her, she was put on edge while firmly being pissed off with all of the anger being pushed at her, "Problem?!" Maggie spat.

Alex was so confused. She kept passing looks to and from Maggie and Kara.

"I don't see a problem here." Kara said sarcastically, shrugging, "Do you Alex?"

Alex went to respond before Kara cut her off.

"Are you going to tell her Maggie or should I?" Kara asked, zeroing in on her.

Alex felt the rift between them and knew this wouldn't end well.

"What are you on about?" Maggie laughed with nervousness, "It would help if I knew where you were going with this...thing."

"If only my sister, your fiancé knew about who you really were." Kara sneered.

"Kara stop it!" Alex snapped.

Maggie now knew where Kara was going with this, and her glare was just as bad as Kara's. Maggie squared herself up to Supergirl even though she knew she would never win against the girl of steel.

"Will one of you tell me what is going on?" Alex asked them both.

"Don't you dare!" Maggie sneered at Kara.

"Why, because lying is better? I can't let you hurt my sister. I came first. Not you." Kara sneered, before turning to Alex, "She works for CADMAS, isn't that right Miss Sawyer?"

"Maggie?" Alex asked her, more or less astounded, and heartbroken.

"I've no idea what she is talking about." Maggie said sternly.

"Oh I think you do." Alex sneered, "I know when Kara is lying and she is telling the truth, why keep this from me?" Alex was reaching for the gun on her hip, but gave Maggie a fair chance to explain, but as she continued to ignore Alex, Alex handcuffed her. It broke her heart, but she couldn't take chances.

"Come on." Alex said with authority. She lead her down to a holding cell, "CADMAS...I don't believe it...I will never believe it. You need to start talking."

"And then what Danvers? You imprison me?"

"You asked me to marry you! I love you Maggie and you keep this from me?" She said, as she held back tears.

"Why does anyone lie? To protect those they love." Maggie said pointedly.

Alex went quiet, and left the room.

* * *

 **Please tell me what YOU think, I have no idea where to take this. I haven't written in a while, so feedback would be great. I'm thinking about maybe using prompts, however, I'd like to make this angsty and have lots of feels.**

 **Thank you for reading :)**


	2. Confessions

"I'm trying to get my head around it. Maggie, you..." Alex began as she sat beside her cell. It had been an hour since Kara confessed all, and now Alex wanted answers.

"It was a covert operation, it doesn't mean-"

"How many died?" Alex asked immediately.

"Excuse me?" Maggie laughed in disbelief.

"Well." Alex shrugged, "It is CADMAS and since you're not denying it, I want answers. I want to know why you lied, what you want from me and what you planned to do with Kara the moment that I'm not looking." Alex demanded, trying to stay as calm as possible.

"I never planned on hurting your little sister Alex, and like I said before, I lied to protect you, and Kara. As for how many I've killed, that doesn't matter. What matters is here and now." Maggie said depletedly.

Alex shook her head in sheer disbelief before standing up, "WHAT DO YOU WANT?! WHAT THE HELL DO CADMAS WANT?!"

"Al- I don't...I love you, that hasn't changed. I'm not with you because of your alien sister, I'm with you because I love you."

"What about those at the alien bar. The 'Gaylien bar as you put it, are they safe? Were they safe? Or did you give them over to CADMAS?" Alex sneered.

"What? No. I'm not as mad as Lilian Luthor. I would never put my friends in danger."

Alex laughed, "I honestly don't know who you are. CADMAS hate every alien on this planet. I hardly think Lilian Luthor would just let them all just walk. Back to my main question, how many did you kill and how many from that bar?"

Maggie sat back down and put her head in her hands, and let out a deep sigh, "Alex, this isn't anyone's business." She then stood up again, watching as Alex gradually lost her temper, "I get it's your business, and the DEO'S but this was all way back when...When life was simpler. Then you came into my life, you and..." She shrugged as Kara walked in, in her Supergirl uniform, "Your alien sister."

"Oh Maggie, stop pointing out the obvious and start giving us some answers." Supergirl snapped, "How long? What do CADMAS want and what do you get out of it?"

Maggie paused and stared at Alex, her love was still there and she doubted it ever left. She contemplated her next answer, knowing Alex would probably want to kill her with her bare hands. With hesitation, she eyed the two women, "Okay." She sighed in defeat, "You want the truth?"

"Oh my...What the hell do you think we have been stood here interrogating you for? Of course we want the truth! Preferably from the beginning." Alex snapped.

* * *

 **November 2012...**

 _"I applaud your every effort to solve this case detective...You must understand these attacks are becoming more and more frequent..." Maggie said on the phone to the head detective of the time. She was sat at home, after a busy day at work, "Promoting me? He can't be serious...Head of what? You are kidding me right?" She turned when she heard a knock on the door,"Look, I've gotta shoot I think my dinner has arrived and thanks once again for the news...goodnight to you too..." She looked down at the phone with a smug smile on her face. She then walked over to the door wearing nothing but pyjama bottoms and a saggy t-shirt. She opened the door and stared at the blonde woman, "You are not the delivery guy...What can I do for you? No, who are you?"_

 _The blonde smiled smugly, "Lillian Luthor, head of the anti-alien organisation; CADMAS. May I come in?"_

 _"Depends on what you want." Maggie said sternly._

 _Lilian pushed past her, "You agree that alien attacks are getting more and more frequent...Yes?"_

 _Maggie turned around and folded her arms, "Humans are defenseless, we don't even know how many there are."_

 _"Which is where we come in. Our aim...eradicate the filth and get our planet back. This is our home and we won't stop until we get it back..." Lillian said as she looked around before facing Maggie, "My question to you is this...Maggie Sawyer, would you like to go undercover...Join us at CADMAS? Together we can claim back what is ours and with our help.." She walked towards Maggie, "You can kill all the threats and we can make it look like you are still on their side..."_

 _"Wait, you're asking me to kill aliens...I do it behind the forces' back, and your organisation cleans up the mess and makes it look like I'm the good guy?" Maggie asked, astounded by what is happening._

 _"Yes." Is all Lillian said in response, she then shrugged, "Although if you don't want to, I can make sure that you and I never even had this conversation."_

 _"Wait, I agree that the aliens in this city is getting beyond a joke, but what you are asking me to do...It's basically homicide, that's what you're asking me to do...This is one hell of a Vendetta..." Maggie said, disbelief taking over. She then turned toward the apartment window, clearly debating with herself what to do._

 _Lillian followed her with her eyes, "We do what we must, otherwise what will happen to the human race when we let our guard down? We can't just let the aliens take over...Maggie, you have skill and, congratulations on your promotion by the way."_

 _Maggie quickly turned, "How did you-?"_

 _"We need you Maggie...You have grit, determination and we share a common goal."_

 _"And what would that be?"_

 _"We do what we must to get the job done, weather right or wrong. What do you think? We get our planet back, and you do your day job without anyone raising an eyebrow. No one can do that."_

 _Maggie took a deep breath and thought further before nodding, "Yeah...Yeah, I'll do it."_

 _"Good." Lillian said with a smug smile, "If you ever have any personal connections with any aliens, you have to do what we pledge. Eradicate. We'll be in touch." She said before leaving._

* * *

 **Modern Day**

"So you just joined CADMAS the day you got promoted?" Alex spat in disbelief as Maggie told her what happened. She paced back and forth trying to get her head around it, while Supergirl sat against a wall, in complete silence.

Maggie struggled to keep up with Alex as she kept pacing, "Look, I don't have any vendetta against the many aliens in this city, or anywhere for that matter. At the time it was for the greater good, look at what Superman was doing. The time he was controlled by Red Kryptonite, everyone was in danger. We only knew it was a matter of time before we were colonized by aliens so we had to prepare for the future. The threat...It was too great, I did my missions, and yes it was murder but it meant the human race kept going."

"No." Alex replied, "Humans are frightened of change and so are CADMAS, if we die out, that's kind of okay."

"At what rate are you speaking?"

"Thousands of years."

"What if it could happen in the space of a few? Alex this isn't about the humans taking revenge, this is about the human race protecting what is rightfully theirs."

" _Rightfully theirs?!"_ Alex spat once more, "We don't _own_ earth, we are just a part of it. We aren't waging war on them and neither are they to us. We just want to live together without fear. We all want to be accepted. Yes when Superman was under the influence of red Kryptonite it made him dangerous but that only accounts for one alien out of many, many others."

"Colonizing?" Supergirl spoke up, "I only came to this planet because my parents sent me here for my own protection because Krypton was about to self-destruct. I lost my home. Kal-El and I lost our home, we only came here to live peacefully. People like you think that all aliens want to do is take over. Will you just listen to yourself before you _think_ you know what you are talking about?" She then stood up and walked over to Alex, and stood beside her, "I'm a hero, I'm using my powers for the good."

"Yeah, until the next time you don't get your own way." Maggie laughed.

Alex frowned, "She was under the influence-"

"Red Kryptonite, I get it." Maggie hissed, "I never wanted to hurt Kara, I never have. CADMAS know that."

"Then why haven't they tried to kill you then?" Alex asked with her eyebrows furrowed in confusion.

"Watching the Kryptonians suffer...They like that..."

"That's sick." Kara spat.

"If it was down to me, had I not met you Alex, I would have killed her the first time I set eyes on her." Maggie replied straight without hesitation.

Both Danvers were now fueled with anger, it was clearly written on their faces.

"I'm going to go and stop some crime." Kara sneered, glaring at Maggie with her eyes glowing, before walking out.

Alex followed pursuit.


	3. Heartache

Kara walked to work the next day, fueled on anger. Probably not the best idea, but Kara had a job to do and she was damned if she was going to let the events of the day before get to her. When walking through the lobby, she couldn't hear Cat's arrival just yet. Instead she headed straight to the only person she felt she could trust. She walked over to Winn's desk quicker than light,minus the super powers. Kara leaned down to Winn, "Can we talk? On the roof?"

Concern suddenly struck Winn as he went to reply, "The roof?" Before he could ask, Kara was gone, "Why is it always the roof?" Winn muttered to himself before leaving to indeed head for the roof. "Kara, are you okay?" Winn asked as he walked over. Kara had her back, faced to him as she looked into the horizon, over the hustle and bustle of National City. Winn walked cautiously over to her, "Alex asked me to keep an eye on you, what's up?"

"I got told something yesterday and...The only person I can trust is you." Kara said plainly, before shrugging, "Hell, I can't even trust my best friend...My other best friend obviously." She laughed lightly, before taking a breath, "Metallo...Yesterday he told me that Maggie had been working for CADMAS..."

Winn was confused, "Maggie, as in, _Maggie?_ She is meant to be one of the good guys, why would she?"

Kara shrugged, "I soared back to the DEO when I was told. I broke her heart Winn...I broke Alex...Who would have thought that I'd be the one to break Alex's heart?"

"I'm sure she would have understood, considering the circumstances..." Winn said softly, "And she will feel awful for a bit, but she will come around."

"She didn't even come around for sister movie night last night."

"Wow.." Winn replied with shock, "She never misses that for anyone."

"I keep thinking about something Maggie said last night, why she lied...She lied to protect those that she loved...I keep thinking that I would have been better to lie to Alex, you know? Act like nothing was going on. I should have lied to protect her."

"But then Maggie would have carried on hunting down aliens and killing them, I assume. Eventually she would have come after you."

"She said that had she never met Alex she would have...I don't know who I can trust." Kara sighed, trying to stop her lip from trembling, "I can't even trust Lena anymore because..." She shrugged.

"Hey, you can trust me, I have your back. Superfriends together." He smiled.

Kara laughed and leaned against him, "Thank you Winn."

"What are friends for?" He smiled.

Kara used her super hearing and heard Cat's voice, "The boss is here. She is at the bottom of the building."

"Let's get to the office...Did you get her an Espresso from Noonan's?"

"Shoot." Kara cursed, "I can be super quick."

"Up up and away?" Winn smiled. Kara smiled in return before leaping from the building.

* * *

Later that evening Kara went to Alex's apartment and knocked on the door. When Alex refused to open, she used her x-ray vision, "Come on Alex, please listen to me."

"What is there to talk about? I've lost everything." Alex replied with a voice that Kara knew was only deep anger and sadness.

"You know this isn't the way." Kara said and pressed her head against the door, "You haven't lost me."

"She got me to be who I really was and now I think it was all a lie. She didn't love me. She used me to get everything she knew about the DEO and pass it on to CADMAS." Alex replied and noticed Kara still hadn't come in, even by the sitting room window, "You're not in here yet and the window is wide open."

"I don't feel like flying." Kara shrugged on the other side of the door. Moments later she heard the latch and walked in, seeing the true extent of pain and heartbreak on Alex's face. Truth be told, Kara's heart broke for her. "Alex." She sighed.

"Everything I am is a lie. I'm not lucky, I'm not fortunate. You know what I am? I am everyone's go-to when they want something. Oh yeah, agent Danvers will sort it out because she will do anything for anyone." Alex hissed as she poured herself some more whiskey.

"You know that's not true." Kara said to her with a sigh.

"Oh of course it is!" Alex growled, "You ruined my life the moment you landed on this planet! As soon as you came, I lost my dad! I lost EVERYTHING BECAUSE OF YOU!"

"Ale-"

"I only got a job at the DEO because of you. My life was fine before you came into it!"

"Okay." Kara said sternly, "You are starting to sound like-"

"Like what?!" Alex spat in her face, now standing merely inches close to her. So close that Kara could smell the strong whiskey on her breath. Alex pushed her back, and Kara really did not know what to do. She didn't want to hurt Alex, so she took whatever abuse Alex was giving her.

"You're starting to sound like CADMAS!" Kara snapped.

"Maybe what they stand for is right." Alex said, with words beginning to slur. This struck a chord with Kara, and it hurt, "Alex, you're drunk and you know that it's wrong. You know that what you're saying is wrong. CADMAS are everything you despise."

"No, they are everything you despise because you're a stupid alien."

"I'm your sister!"

"Really?" Alex laughed, "You've never been my sister. From day one I hated you. You basically waltzed in and took everything I care about from me. You and I are nothing to each other. You hear that? Now get out."

"No Alex." Kara said sternly as she fought back tears, "You need to get sober-"

"Get out before I find some Kryptonite and do some serious damage."

Kara took this as a serious threat, and shook her head, "Okay, I'll go...I will check on you first thing."

"Don't bother." Alex spat, "Get out of my life. If you don't I will expose your true identity."

"You're bluffing." Kara replied with her voice trembling.

"Really? Let's see how miss Luthor takes the news that her only best friend has been lying to her. She probably wouldn't take lying very well...She'd probably want you out of her life like I do."

Kara took this as her cue to leave, and so she did. Slamming the door behind her. As she walked down the hall, she felt a lump rise in her throat. Heartbreak, only like she had never known before. She had to get her sister back, but how she was going to do that was beyond her.


	4. Deep

A month following the events of the true Maggie being exposed, J'onn had to let her go on the grounds of human rights. He knew that she was a danger to Kara, but because she was human, he had to let her go. Kara hadn't seen Alex for four weeks and the three women were torn apart. To say there was a family there before, it was certainly gone now. Kara spent most days as Supergirl, she began to forget who Kara Danvers was, and to Winn, and J'onn, it was a terrifying prospect. Most days she just walked in, had her fair few missions and sat on top of a tall building on her own. Slowly slipping into the abyss. These days Kara liked to pretend that she wasn't real, that no one cared.

That was easier than letting her heart get broken.

Alex walked into the DEO the day after Maggie was released, and Kara looked at her like she had never met her. Today was the first day in four weeks the pair had actually set eyes upon each other. Alex looked right through Kara, and Kara felt a lump forming in her throat as she stared at her older sister.

 _It's easy to leave than to be left behind._ Kara thought to herself as the orders had been given. She watched Alex leave, and the silent treatment truly hurt. Kara stood there unaware that J'onn was talking to her, "Supergirl, did you get that?" He asked. As Supergirl came out of her dazed state, she nodded, "Kick alien butt. I've got it." She said before walking off.

J'onn and Winn exchanged concerned looks as Kara walked off.

* * *

Alex called Supergirl over the radio, and she quickly zeroed in on their target, "I've got it." Supergirl replied through the radio and after a few punches had the suspect detained, "He was nothing on Metallo." She laughed, and watched as Alex walked over, "Good job Supergirl." Alex congratulated, treating her as a fellow agent, and nothing more, with a tone that was dry.

"Alex." Kara said pleadingly as Alex began walking away. Alex turned around slowly and let out a steady breath, "Supergirl?" She asked straight up. Kara was in pure disbelief, "Hey, what about Kara?"

Alex finally locked eyes with her. The look in her eyes frightened Kara. The response was even worse, "I don't know a Kara, I only know Supergirl."

"And who is she to you?" Kara asked, trying to stop her voice from trembling. Alex's dark eyes still did not change, "A fellow agent. Nothing more. You do your job and I do mine." She said sternly before walking away. Kara was frozen. The tears came to her blue eyes quicker than before. She shot herself into the sky. Alex looked up as Kara vanished, before getting into the van to return to the DEO.

* * *

"Where is Supergirl?" J'onn demanded as he saw Alex returning to the DEO. Alex continued walking through the command centre, "She shot up into the sky sir."

"Alex." J'onn said as he stopped her, "I know there has been things going on between you and Kara since Maggie was exposed. Kara has become even more withdrawn. On human standards, I'd say she is depressed. She is never home, she never goes to work and only responds to 'Supergirl'." Alex shrugged as she looked up at the projected image on the huge screen above her, "Sir, what Supergirl does is her own business. She has her life and I have mine."

"You are meant to be sisters." J'onn growled. Alex was having none of it, "My life was a lie sir, I'd prefer it if Supergirl and I had our own lives and we were kept apart. She ruined my life enough. Now she can stay out of it." She snapped. J'onn gave up and turned to Winn, "Mr Schott, track Supergirl, find where she is."

Winn tapped away at his computer and his eyebrows raised, "Okay...This is a rare thing. L-Corp. She's gone to see Lena. She has not done that in weeks, should we be concerned?" J'onn and Alex looked up at the board. "Get a team down there on standby, just in case." J'onn ordered before walking off. Alex followed him, "This is a waste and you know it!" She snapped. J'onn glared at her, "Go home Danvers!" He snapped.

* * *

Lena looked up as her assistant, Jess walked in, "Miss Danvers to see you Miss Luthor." Lena looked up from her desk, with a smile spread across her face upon seeing Kara dressed in her civilian clothes, which was also another rare sight. "Kara." Lena smiled, "I have not seen you in such a long time. I hope everything is okay."

Kara smiled slightly, "Work, Miss Grant. I've been up to my neck with paperwork and getting scoops." Lena stood up and Kara waved her arms, "Please, you don't need to get up for me." She smiled, as she took a breath, "Actually, I have something to tell you."

Lena frowned, but her smile didn't falter, "Anything."

Kara removed her glasses and untied her bun. She then proceeded to unbutton her naval blue shirt. Lena's face dropped as she saw the symbol of the house of El appear. A lump formed in her throat, "Supergirl?" She gasped in disbelief. Kara merely nodded, "I'm her." Lena was conflicted, she didn't know weather to smile or to kick her out, "You lied this whole time?" Was the first thing she asked once all of Kara's buttons were undone. Kara took a breath, "It's funny isn't it, my sister's fiance lied about who she really was to protect Alex...And I lied to you to protect you."

Lena was frozen. "You were the only person I trusted." She said with her voice trembling, "You hid yourself because I'm a Luthor, you kept it hidden for this long and you...what? Want me to accept it with open arms?" Kara stepped forward towards her, "No, no that's not what I expected. I'd like you to see it from my point of view."

"Oh I do." She said with a tone that was not reassuring, "You used me to get what you want, and now everything is different. You are like everyone else. You use me and then you leave me."

Kara shrugged, "I'm beginning to think that...I've lost everyone I love. I go by Supergirl more than ever...In fact I'm starting to believe that...Kara Danvers was a mistake and Supergirl is all I am. It's all I'll ever be."

"That's all you should be." Lena said sternly, before sitting at her desk. "You can leave the same way you came in, _Supergirl_."

Kara turned to the door and buttoned her shirt, and put her glasses back on before leaving.


	5. Vacation

After returning from Lena's office, Kara decided that she needed a break from everything. "J'onn." Kara said in a plain tone, he turned around with his hands on his hips, "Supergirl, what can I do for you?" He watched as she walked past Winn, frowning at her demeanor. Kara stopped next to him, frowning at Winn as he was giving her suspicous looks too, "I'm uh, I'm going away for a while. National City can manage a few weeks without me I'm sure. I just need to clear my head of everything that is going on." She said, before noticing the way Alex was looking at her, "Sir, I just-I need a break."

J'onn merely nodded, "Okay Supergirl, but first I'd like to know why you were at Lena Luthor's office." Kara then shrugged, "She needed to know some truths and now she knows."

"Truths?!" Alex snapped, "And what does she now know?!" She walked over to Kara, with anger all over her face. Kara took a breath and looked between the two, "She knows that I'm Supergirl." J'onn instantly glared at her, "Do you realize how stupid that was?!" He growled, "How are we meant to protect you now that-"

"J'onn, I don't need protecting. It's better she knows the truth." She said before she looked at Alex, "After all, we know what hiding the truth does to those that we love."

"You are stupid, you know that?" Alex growled.

"You were gonna expose me anyway, so, it's best she heard it from me. I'm going away for a few weeks, like a little vacation."

"Where will you go?" J'onn asked.

Kara shrugged, "England? Poland, I don't know."

"We can't protect you." Alex emphasized.

"I know Alex! But you are ignoring me and my whole world is crashing down and I need a break."

"Your world is crashing down?!" Alex snapped.

"ENOUGH!" J'onn growled, "Supergirl, go. Go on your vacation. When you come back, your attitude better be changed. As for you Agent Danvers." He said, turning to her, "You need a break, take a few days out."

"But sir-"

"Out, Danvers." He ordered. Alex finally did as she was told, firmly backing down. She pushed Kara out of the way with her shoulder as she left.

* * *

"Daughter, you did well." Lillian smiled as she walked over to Lena. The warehouse space was dark, cold and damp. Lena stood her ground clearly, not wanting her friend to get hurt, "You bugged me. You knew that she was losing it, you only knew it was going to be a matter of time before Supergirl exposed who she really was."

"Oh no dear, I knew long before you did. The bugging was a fake, you needed to find out the truth for yourself. She is callous, and mindless. You think she cares about you?" She asked as she walked over. Cyborg Superman was stood in the corner of the room while Metallo stood with a firm smirk on his face. "Supergirl is the bad guy here, not us."

"She is my friend." Lena said sternly, "Yes I was hurt but...She is on her own. She needs someone."

"A Super and a Luthor working together?"

"We did it before when the Daxamites were on earth, however, I found that I was only useful for one thing. Being the bait in your evil plans. You've never loved me so don't act like I was ever something meaningful to you. The only person who means anything to me is Kara!"

"Oh, she's an alien like the rest of them, isn't that right, Sawyer?" She said with a smirk and turned around. Lena frowned at the sight of Maggie, "Maggie?" She gasped in disbelief, "What is going on? I'm...confused."

"I used to...I work for CADMAS, I have done for years. The difference is, I never wanted to hurt Kara." Maggie said as she walked in, wearing only black. From black combo trousers to the thick jacket that completed the look, "Had I never known Alex, I would have killed her."

"Only, you are going to kill her." Lillian said with a smirk, before pointing at her own neck, "You have a chip right there and if you refuse to kill Supergirl, you die too and Alex Danvers, oh that stupid agent from the DEO, will lose you forever."

Maggie felt fear strike her worse than before, "Alex can't lose me. I wanted out some time ago and you know that!"

"And then you got into a relationship with a DEO agent, and look how that turned out. I told you the deal the day we met, and that has not expired."

Lena glared at Lillian, "You could just leave her alone."

"But then, how would we get what we want?" Lillian sneered as she turned to her, "Lena, daughter." She said as she took a breath. Cyborg Superman quickly had a grip of Lena, and now Maggie was terrified, "LEAVE HER ALONE LILLIAN!" She shouted. Lena struggled in his grip, but kept herself strong and firm.

"It has transpired that there are only two ways to kill Supergirl. If one of you fail, we always have a back-up." Lillian smirked, delighting in all that was going on, "We are going to create a meta human. Or a hybrid Kryptonian, whichever works best, and you will bring Supergirl down."

Maggie watched in horror as Lena was injected with green liquid that made her scream in agony, "LENA!" She screamed, running to help her. Lillian only laughed as Lena collapsed to the floor, "This is all bitter-sweet, but a mother has to do what she must to protect her child." She smirked before turning to Maggie, "If she doesn't complete the task of killing her, you will." Maggie looked up as she cradled Lena with only fear present in her eyes.

* * *

 **2 weeks later**

"Alex, Alex, Alex!" Supergirl shouted with excitement as she walked into the DEO, in higher spirits than before, "Guess what? I went to England and is was _so_ amazing! I went to their countryside and there is so much of it. I went to this place, it was a county I think, and it was called Lincolnshire, and there was so much there! Alex I wanna live in the countryside. It's so good!" Alex looked at her, only smiling at her, "Oh, so English countryside did you some good, did it?" Kara nodded, "Yep. Alex you should see the agriculture and everything. They were having this event on this huge field and when I say huge, I mean, I want a garden that big..."

Winn frowned, but was glad that there was no tension in the air. Alex took Kara's shoulders and tried to hold her down, "Kara, look, I'm sorry about what was said, and what happened a few weeks ago. I was a huge jerk and I shouldn't have treat you that way." Kara only smiled, "Alex, it's okay, honestly. You were a jerk, but you lost Maggie, it's understandable. Anyway, I brought some things back." She said jumping back into her talk about her vacation.

"Winn." Alex said to him, "Look up, this thing that Kara is talking about, what was it? The Lincoln-"

"Lincolnshire show, on their showground. Alex it's so good! I mean, apart from when it rains which is a bit bad, but apart from that, everyone is just so nice!" Kara said, forever glowing. Alex couldn't help but smile at her, she hadn't seen Kara like this for a while and it was very refreshing.

"Okay...Lincolnshire show." Winn said as he brought it up, "Wow, this is actually quite neat. I'm not even going to lie, even I would want a vacation there." Kara only squirmed with excitement with Winn's response, "It's so cool!" Kara gasped. Winn only frowned, "You know that Lincoln is a city right?"

"Yeah, it has a Cathedral and everything but the surrounding countryside is so beautiful!"

"You wanna know about the Lincolnshire show right? Okay so, the Lincolnshire show happens every year, I believe on the 20th and the 21st of June and it has been going for 133 years, now that is amazing. It hosts agricultural themed events with the obvious stuff, shopping, music and food-" Winn was then cut off by Kara. "The food was just _amazing!_ They even have their own sausage which tastes amazing too!"

Winn then continued, "Competitions, farming...basically a really fun day out for the family."

"We should do that." Alex agreed, "But next year now."

"Really?" Kara gasped with excitement.

"Yeah, why not?" Alex smiled, "I bet you cleared them out of their food too."

"I might have..." Kara said, trying not to look guilty.

"Wait, did you find something better than Potstickers then?"

"No." Kara said, as she shook her head. Alex merely nodded, "Okay then." She smirked before an alert showed on the screens.

"Oh no." Winn muttered, "Kryptonite radiation within the DEO. We have an intruder."

"Lockdown protocol." Alex ordered, as Winn located the source. Alex turned to where it was coming from and saw Maggie standing there. Alex drew her gun, "Maggie. Stay where you are."

"I'm so sorry Kara, Lena is in danger. "

"Lena." Kara gasped, "What happened to her?!" Maggie stay stood where she was, forcing back tears, "I'm sorry Kara." She said before shooting Kryptonite from her chest, blasting Kara to the other side of the room. Alex didn't know what to do, she was frozen where she was, Supergirl was not an option, with her already hurt. Someone had to get the situation under control, but either way, Alex knew Maggie was done for.


	6. This is it

"Maggie just stop! Think about what you're doing!" Alex pleaded, forcing back tears but her gun was still pointing firmly at her. Supergirl was struggling to get up, the huge amount of Kryptonite she had just been struck with was overwhelming to say the least. Alarms were blaring and soldiers were dispersing. everywhere. Alex's head was in too many places, "Maggie please!" She pleaded again.

"It has to be one way Alex." Maggie said pointedly, "I should have saw this coming." She shrugged, "And if I don't kill Supergirl, Lena is next on their list and you know how much Kara cares about her. It was too late to save me, but what about her?"

"Hold your fire!" Alex barked at the soldiers surrounding them. She then turned back to Maggie, "What about her? What about us? We were supposed to be getting married and I believed that everything we had was perfect! It was too perfect to be true wasn't it? I can't live a happy life, I've never been able to. But the times we shared together...were they real?"

Maggie stood silent. Her chest was glowing the brightest green Alex had ever seen. Maggie hesitated for a moment, "They, they-what we had was real." She smiled as tears swelled in her eyes, "I love you with every piece of my heart Alex. My heart belongs to you and only you. You changed my life, you made me happy." She smiled, sadness was clear in her eyes, and it broke Alex's heart. Alex lowered her gun and slowly moved towards her, "Maggie, you have to stop this."er

"Supergirl, are you okay?" Winn asked as she helped her up. Kara looked up, staring at the scene unfolding before her. She was injured, blood dripping from a gash in her lip, "I'm-I'm fine." She said slowly as she finally got her balance, "Maggie is beyond my help now. I need to save Lena." Winn suddenly panicked, "No, Supergirl you can't." Kara glared at him, "Alex has lost everything. I'm not letting my best friend suffer, Winn."

"I have a job Alex, a mission." Maggie said sternly. Alex carried on traipsing towards her, "To kill my sister, I know. But you said before." She said, before shaking her head, "You wouldn't because she's my sister." Maggie finally looked into Alex's eyes, "If I don't, I will-"

"I know." Supergirl said as she walked over. Winn looked on in horror, terrified of what will happen to Kara, standing right in front of the enemy, "I'm sorry Maggie." She said carefully, watching how she was going to form this sentence, "But you've already lost, and deep down, you are still human enough to know that now...You can't go back."

"You want to save Lena right, your best friend? The only way you'll do that is if I kill you." Maggie said sternly before the green in her chest began to load up and surge again. Alex turned to Kara, "SUPERGIRL GET OUT OF HERE!" She shouted. She then put her hands on Maggie's cheeks, "I love you so much, that will never change, but please. Tell me, tell me where Lena is so we can save her. What is CADMAS up to?"

"Half Kryptonian..." Is all Maggie said, before collapsing. Alex caught her and lay her down in her lap, "Come on Maggie." She urged, forcing back tears, "Be a hero. please." Alex had a tight hold on her as the green in her chest began to lose it's glow, "Lower National City...They are hiding...Lena isn't human anymore..."

"The hybrid." Alex said in realization. Maggie nodded. She then reached into her pocket and pulled out a blue emerald, "Use this...it'll help you find CADMAS...They injected Lena with green Kryptonite, but it hurt her...It's supposed to be harmless to humans...they did something to it...tampered with it. Alex, find them and destroy them." Alex nodded, "I will, I promise." Maggie then smiled up at her, "It was great knowing you Danvers." Alex then realized what she was saying, "No Maggie, you have to hold on."

"They are draining my life from me...You know that I won't make it out of this." Maggie said weakly, "I would have loved to have been Mrs Danvers." She smiled. Alex only laughed, before kissing her. The kiss was long and passionate, and Alex wanted it to last forever. As she pulled away, Maggie whispered, "I love you." In her ear and as Alex replied back to her,she was gone. Alex was fueled with anger beyond anything she had ever felt before. Everything was burning. She slowly lay Maggie's body on the floor, and the moment she caught sight of Winn, the first thing she said was, "Locate CADMAS now." She said it in such a tone, it frightened Winn almost half to death.

Winn was back at his computer quicker than ever before and drew the lights up, deactivating the lockdown. Alex stood over Winn as the blue crystal flashed. The moment she saw the red dot on the screen, she was gone, "I need a squad on site now. Be careful, it could be dangerous." She then activated her inter-com, "Supergirl, can you hear me? We have located CADMAS."

"I hear you loud and clear Alex, is Maggie-"

"Maggie's gone." She said, keeping her tone strong. Throughout the room, there was a deathly silence. Winn stared dishearteningly at his screen as Supergirl also stayed quiet. After a few seconds of silence, Alex spoke again, "It's up to us now." There were a few more seconds of silence as J'onn looked over to Alex. Alex was thinking about everything she had just witnessed in these last few minutes and finally declared, "This is war."

* * *

 **A:N: This is getting so interesting, right? Thank you all for reading, a new chapter will be up soon. Thank you so much for the feedback and everything! See you soon! :)**


	7. This is War

_This is war._

 _This._

 _Is._

 _War._

Words that echoed in Supergirl's ears as she soared through the sky. The world stopped.

Everything stopped.

The sky was grey, and rain was pelting Kara. She swallowed the lump in her throat and closed her eyes briefly for a moment. Visions of the events that lead to now. Alex had started a cataclysmic event, war. It not only waged on CADMAS and the DEO, it had spread further than that. Human and alien casualties alike. How they could all come back from this, no one knew.

It had been a month before Alex made the declaration, and there was no taking it back. It was never meant to go this far, but Alex was fueled with anger, and revenge was the only way she thought she could get through the grief of losing Maggie.

Supergirl landed on the pavement, well, what was left of it. All around her, there were smoldering fires, burned out cars and buildings cracked and torn, threatening to fall. Where were the people?

Gone.

As Kara looked around, everything around her may as well have been an echo of Krypton on it's very last day. As Kara walked through the rubble, she found it hard to keep herself together. All the radio com's were dead.

Silence.

Taking a deep breath, Supergirl carried on trudging through the concrete. The shattered concrete that may as well be tiny pebbles. Tears stung her eyes as she carried on making her way through a street, "How could it have come to this?" She asked herself. She looked up, and saw the huge 'L' on the building for L-Corp had fell and was in a 90 degree angle. Supergirl flew up, and put it in the right position. As she stared at the giant 'L', she felt like there was a huge piece of herself missing, "I'm sorry Lena." She said out loud. She then turned and once again looked at the billowing smoke coming from the buildings below her.

* * *

"Our darkest day has already happened." J'onn announced to everyone in the DEO. Winn sat in complete silence. He now had stubble on his face, he had lost hope in the human race. He was solemn, and had become withdrawn since the destruction that occurred only four weeks ago. J'onn was less authoritive, and could hardly look at Alex. He was ashamed, he watched her destroy her own world and he was full of sorrow and mourned this planet like his own. He never thought he'd see the human race practically end itself and what made it worse was that it was because Alex, someone who J'onn considered family, took it upon herself to decide the fate of the human race.

Alex walked over to Winn, "Status on-"

"The same as yesterday, the day before and the day before that. There is nothing Alex. Lillian Luthor is still out there, but what is the point when there is nothing left to fight?" Winn replied. J'onn briefly looked over, "He's right...We have no cause."

"But maybe if we-" Alex started.

"The human race, and aliens have gone underground. Supergirl is alive, and Maggie is not. Alex, I would have stopped you-"

"Then why didn't you J'onn?"

"Because you wouldn't. I had to protect you and Kara."

"And we have single handedly destroyed the human race. Not in a matter of centuries, days." Winn replied, "Maggie tried warning us, now look where we are. There is nothing."

"I'm closing the DEO down. We have no longer got a cause." J'onn said to them, before looking at Winn, "Mr Schott, close everything down."

Winn looked up at Alex, and she was staring at J'onn. He walked off, and she stood frozen. _What have I done?_ Alex thought to herself.

* * *

Kara walked down the sub-way line and all she could hear was dripping water. The silence terrified her. No human or alien in sight. She hit the wall in anger, "How could you do this Alex?" She gasped, breaking down. She hit the wall a few more times, before falling to her knees, sobbing. She stared at the deserted rail line in front of her, and then to the earth that was next to it. She saw a faint glow beneath it. She quickly got up and knelt down to it, before beginning to dig. Once she dug far enough, she had a huge smile on her face when she looked at the shiny object and the human inside it. She called Alex, "Thank Rao this line still works. Alex, I've found something."

"J'onn." Alex said to him, "Kara has found something."

"What is it?" He asked, and Kara heard him through the phone.

"I've found the salvation of this planet." Kara laughed in relief and joy,

* * *

 **A:N: Thank you once again, I am thoroughly enjoying writing this. I wonder what Kara has found? :) You will all find out pretty soon I expect.**

 **Thank you :)**


	8. Before the War

**4 weeks before the war**

"Alex, you need to think about what you are doing." J'onn urged her, as she was getting kitted up. Alex was clearly sticking to this. As she put a gun in her holster, she looked at J'onn with fire deep in her eyes, "I lost Maggie, I want my revenge."

"You are declaring war. Have you even thought about this?" J'onn growled. Alex walked past him, ignoring him completely, "I'm taking control now. This is personal. CADMAS think they can walk away with everything that I love and they are so wrong." She sneered before looking at Winn, "Got a clear location?"

"I do, are you not sending Supergirl in?" Winn asked.

"Of course I am." She said with ice in her voice.

"But-she could get killed Alex." Winn gasped. He knew this was getting way out of hand. J'onn stepped in front of Alex, "She is your sister, have you become heartless or so cold that these things don't matter anymore?"

"Of course I care J'onn." Alex growled, "But CADMAS need destroying." Winn then alerted them, "Guys...we have a problem. Supergirl-"

"I'm looking down on it now." Kara replied, "Alex...wasn't Maggie with you a few seconds ago?" She said, frowning at the sight below her. Alex turned and looked at the spot where Maggie was before.

She was gone.

"Crap. She died and now they are using her as a weapon." Alex replied with a sneer, "Like I said." She sneered at J'onn, "War, I fight for the human race. What will you do?" She asked, glaring at him. J'onn stood glaring at her, but did not respond to her. "It's our planet, we must defend it."

"Who are you doing this for Alex?" J'onn asked, "Humans, aliens? Who is your cause?"

"You know the answer to that J'onn. We are all equal, and CADMAS wants to eradicate every life that is alien and they are not doing it in Maggie's name." She said, before leaving with a team of soldiers.

* * *

"We are outnumbered Alex." Supergirl gasped as she stood in front of from what she could count, at least five Metallo's. "Alex, I can't fight this. They have come prepared. They've won."

"Winn, come in." Alex said over to radio, "Activate nuclear missile one."

"What? No. Alex I will not be responsible-" Winn replied quickly. The action was unfolding and he watched as buildings around them were being shot down one by one. Why J'onn wasn't in the field even confused Winn. He then saw government soldiers arriving on the scene. What followed over the next few minutes were screams and cries for help.

Supergirl stay in the sky, staring down at them all. Faint memories of Krypton's last days that haunted Kara when she was a child had come back, stronger than before.

J'onn had his back turned to everyone in the base as he too had flashbacks of when the white Martians were attacking and killing.

Fire.

Bloodshed and death.

A tear fell down Kara's cheek as her super hearing picked up every scream, cry and beg for help. Kara just couldn't, she was frozen. The Girl Of Steel was frozen.

"WINN ACTIVATE THE MISSILE!" Alex ordered. Kara heard the order and only closed her eyes, breathing heavily.

Winn typed in what he needed, and watched as blazes of Kryptonite were shot in every direction. Buildings were collapsing, and the only heroes in the city had stopped. Nothing could be done. They were all outnumbered.

"I'm so so sorry." Winn gasped with a trembling voice as he pressed the enter key. He sat back and put his hands over his face, "Alex the missile is heading your way."

"Alex, you are destroying people. Families, children..." Supergirl said over the com.

"I know." Is all Alex said in response on her way back to the DEO.

"How are you okay with this?" She gasped.

"We were outnumbered Supergirl, we have done what needed to be done."

"By killing thousands of people!" Kara snapped, "This is just like Krypton."

"But it's going to be on a worldwide scale." Alex replied.

"What?" Is all Winn could muster, "Alex, no! J'onn say something!" He pleaded, "I will not be responsible for human extinction."

"Tell them to head underground. Send out warnings." J'onn ordered. Winn stood up and moved away from his computer, "Sir, no. I'm not...I will not do this."

"Mr Schott, agent Danvers gave you your orders." J'onn said in a voice that wasn't as strict as it normally would be.

"Agent Danvers." Winn ordered, even though it was not his place, nor his predicament, "Stand down. I refuse to end humanity."

There was then silence over the coms.

All three were frozen.

As Alex walked back into the base, there was a huge boom. Kara was frozen.

All of the screaming stopped.

 _Silence._

Winn was frozen, as were Alex and the rest of the DEO. Kara stared at the mushroom cloud as tears streamed down her face.

"CADMAS wasn't even destroyed." Kara said after five minutes over the surviving com, "The power of humanity. Put an idiot in charge of a weapon of mass-destruction...and this is what happens...Alex, you just single handedly wiped out a whole city. If you'd all excuse me, I need to go to another planet. This one makes me _sick."_ She sneered, before the line went dead.

* * *

 **A:N: I am enjoying this a bit too much, why J'onn and Kara didn't help and where was Superman? I believe that maybe they decided that it was finally time to let humanity see what they are truly capable of. I have left this open to other opinions. It's kind of rhetorical, so any conclusions as to why the aliens didn't help is open to question.**

 **Thank you for reading. :)**


	9. Aftermath

**Present Day: Kara finding the Salvation to the human race.**

"I've found the salvation of this planet." The smile and joy upon Supergirl's face could not be much more joyous.

"What is the salvation to this planet?" J'onn asked even more confused, "Supergirl did you did you find any humans down there?

Kara activated her super hearing, "I can hear some voices. People must've known before the missile. When the Metallo's began their attack. Some escaped and made it down here. How they've survived I don't know. There must be aliens down here that can produce food so that everyone can survive off of each other, but back to the main thing, well, the second main thing." She laughed, "I've found her."

"You've found who?" Alex urged.

"I've found Lena." She smiled, "And she's alive...Lillian must've buried her while...I actually don't know...But if she is a hybrid...She survived."

"And how is Lena Luthor the salvation of the planet?" Alex asked, with confusion in her voice. Supergirl frowned, "She is the smartest person remaining on this planet, well, other than Miss Grant."

"Wait, Cat Grant is alive?" Winn chirped.

"Yep." Kara laughed as she lay Lena's body on the platform. Kara had never been happier, "There is hope."

Lena began to stir, "Ka-Kara?" She winced, finding the light too bright. Kara smiled and put her hand on her cheek, "Hello." She smiled, "The air up there is still toxic to humans...We need you to clear it."

"Why, what happened?" She asked, her voice still dry.

"Well, the DEO...They nuked National City to protect the rest of the world and luckily Alex didn't declare war on the rest of the world...You are the only person I know that can save us. Please Lena." Kara asked softly. Lena smiled as she was finally able to look into Kara's eyes, "Hey, did I tell you how beautiful your eyes were?" Kara laughed and kissed her forehead, "Should we get going?" Lena merely nodded, "Yeah." She then let out a small smile. Tears of joy fell down Kara's face as she sat with Lena a little long.

* * *

"So how are you still alive?" Alex asked Lena as she sat in the med bay, "I have many questions for you."

"As do I miss Danvers." Lena said sternly.

"Please, don't call me that." Alex said to her in a low voice.

"So, why would Lillian bury you? What did she do to Maggie and why did she have to die?" Supergirl asked Lena.

"Well, the response to your first question, she just does that to experiments gone wrong. That or she knew that someone _stupid_ enough could or would set off a nuclear explosion and she knew that I'd be clever enough to make the air pure again, and make ground level habitable again. It was a case of either aliens lost or we both lost. Well." she said taking a breath, "We all now know what the conclusion to that was. As for Maggie." She began, and Alex's stance shrank. Kara eyed her carefully, "Alex, you don't have to stay if you don't want to-"

"I do." Alex said as she cleared her throat, "I need to know why."

Lena let out a shallow breath, "Lillian made the agreement with Maggie years ago and therefore she was tied to that agreement. No backing out. When Maggie did try, Lillian had the idea of making her like Metallo, installing her with a chip that could control her dead or alive, should she not complete her mission. I think we all know what that mission was." She nodded, looking between them, "I was meant to be the back-up plan, but because I'm..." She then cleared her throat, "I was able to override whatever hold she thought she had over me...I kept my conscience. That's what killed her, she could not switch off my free will with me being a hybrid."

Alex interrupted, "Wait, what? Hybrid? Maggie brought this up, she said something about them tampering with green Kryptonite which is meant to be harmless to humans."

"Lillian kept some blood, which is really weird...because you would have thought keeping it for that long it just wouldn't be useful anymore. Turns out she also had a thing which made the blood as fresh as the day it was extracted. She did something to it. I don't know what, but to make it useful to create a hybrid, she must've used something pretty powerful." Lena continued.

"Wait." Alex said after a minute, "Once Maggie was dead, she was able to use a corpse as a weapon?"

Lena nodded, "She created a device that could...resurrect the dead, but it only worked for those deceased for minutes only. Don't ask me how, it was probably destroyed by the blast."

"How did they drain Maggie to kill her? If she was like Metallo, how were they able to do it...if I were to put it into better words, wirelessly?" Alex asked, choosing her words carefully.

"Should one Metallo die, another harvested the energy and it was passed on, like germs or disease...Just with Kryptonite fueled maniacs, like you were fueled with anger enough to wipe out, almost the entire city." Lena bit the last part, and Alex went to attack her, but Kara stopped her, "She's right Alex, you made that call, you made Winn do that. We need Lena in one piece. Even though she might not be that breakable anymore." Kara frowned. Alex stepped away, "Luthor, get to work."

Lena got up and glared at her, "First I need to know what was in those nuclear weapons."

"Ask Winn, just ask me when you need the resources." Alex said before walking off. Once they were alone, Kara turned to Lena, "So...You're part Kryptonian now?" She asked with a small smile. Lena nodded, "Kara, thank you for finding me." Kara merely smiled, "I'm glad you're still alive...after all of this...hell." She concluded. Lena agreed, "I wasn't conscious for the whole Nuke situation... but as we walked through the aftermath...I can see why aliens would turn their back's on humanity. So does this mean I share your powers too?"

Kara shrugged, "Maybe." She said before laughing. "Let's get to work Lena." Kara smiled before walking to the lab with her.

* * *

Winn stood next to Alex as he watched both girls head to the science lab, "Our salvation. I should have guessed." He said with a small laugh. Alex shrugged, "Hey Winn, I'm sorry for making you do that." Winn was uncomfortable instantly, "This is where I leave." Alex grabbed his arm, "I'm serious." Winn turned to her, "You made me make a choice that no one should make Alex! There may be blood on your hands, but I am astounded at how well you are taking this! You weren't the one to press the big red button."

"Winn-"

"No Alex!" He spat, "I have not been able to sleep properly ever since I did that! How do you do it?! You know sometimes, I actually think you wanted that to happen. You lost Maggie, I get that. You were angry, pissed even, I get that. But vengeance and revenge just for one life when you took- When _I_ took thousands, _thousands_ more! That doesn't equate to anything else. I'm done with this conversation." He sneered before walking off.

* * *

 **A:N: All I can say is thank you. I hope I am tying up loose ends for you. More to come soon :)**


	10. Strange Happenings

"Look, Kara, you can't keep blaming me for what happened." Alex spat as she followed Kara through the DEO, after leaving Lena to create her anti-toxin to clear Earth's air. Kara was beyond pissed, "Alex, you owe everyone who still remains from this an explanation! This thing affected more than National City, and according to Winn, he let off two missiles because you ordered him too after and no one was told! There was no more danger after the first! I deserve a damned explanation!" She snapped, throwing Alex against the wall, "TELL ME!" She shouted, keeping Alex firmly to the wall. Alex winced in pain upon impact, "Kara!"

"Tell me Alex, why did you make this a worldwide affair?"

"It was like insurance, a just-in-case missile." Alex gasped, "Jeez, I think you've dislocated my shoulder!"

"You'll have more than that by the time I'm done with you!" Kara snapped, "You wanted revenge right? I could have just hunted her down and you could have put a bullet through her brain, but no, you had to get trigger happy and destroy the world! Do you have no mercy? No consideration for every other inhabitant on this planet?! Do you know how helpless I felt that day?! I hung in the sky and I heard screams, and cries from everyone and I just hung in the sky! The symbol on my chest isn't worth it's meaning!" She snapped before dropping Alex, "Fix this stupid mess!" She sneered before walking off. Alex stood, rubbing her shoulder as she watched Kara walk away.

* * *

"How's it coming along?" Kara asked Lena as she walked into the lab. She frowned at the small box, which had Kryptonese symbols all over it, "There is no way a box this tiny can clear the air of those toxins."

Lena frowned, "Why do you think I'm making at least five?" She laughed before noticing Kara frowning at the writing on the boxes. Kara leaned down to one of them, " _Hope in a world that was doomed to repeat it's mistakes?_ What does that mean?" Lena looked at Kara, wearing goggles, "It means that humanity has repeated the past...it was a warning and no one listened. Did you ever read about the use of atomic weapons that could ultimately end humanity?" Kara merely nodded, "That was Chernobyl right?" Lena shrugged, "That was an accident, but yes, a weapon like that could end humanity."

"So what you have written on these...is, it is certain that something like this will happen again?" Kara asked, as she stood up. Lena got noticeably fed up, "It has already happened once, well three times. Only what Alex did was reckless, the worst thing is...Kara, don't take this the wrong way." Lena sighed as she removed her goggles, "I think Alex wanted this to happen, she was just waiting for an opportune moment."

Kara merely laughed in disbelief, "Why would she do that?"

Lena shrugged, "She worked at the DEO way before you, maybe she came across something so nightmarish that she thought...Maybe she thought that humanity and alien kind alike should not be allowed to exist."

Kara laughed again, this time more uneasily, "No...Alex wouldn't-she wouldn't...I mean, I'm her sister, her alien sister...If she saw something like that she would tell me, right?"

"Some things are too frightening to think or talk of." Lena said with certainty in her voice and enough confidence to frighten Kara. Kara at this point was very uncomfortable. She had so many questions and some thoughts of what Alex may have seen truly did frighten her, "Yeah, I...I think I need to speak to Alex." She then rushed off to find Alex.

* * *

Once she arrived in the command centre, Kara leaned on her elbows, "Alex...did you want to destroy everything that you did?" She asked out of the blue, watching as Alex worked away on her tablet. Kara took a breath as she got no response, "Look, you worked here way before I came along and...There has to be a reason why-"

Alex blanked her, walking off as if Kara wasn't even there, "Alex, we need to talk about this, because if there is something more-"

"There were five of them Kara, you and Superman could not help and so I did!" Alex snapped, stopping and turning around to her. Kara looked into her eyes and saw something dark behind them, "One missile to destroy the city to destroy them. I understand that, but what about the rest of the world, what was that for?"

"I'm not speaking about this." Alex growled, "Back off Supergirl!" She snapped in an icy tone.

"Alex what have you seen? What aren't you telling me?" Kara asked, "What-what is going on?"

"Nothing to concern you." She snapped.

Kara pushed even more, "Why would you want to destroy the world?"

"I only destroyed it before the stupid other humans could." She sneered. Kara heard something in her voice that time, that was not Alex, "What are you?" Kara asked. Alex then walked away, "Apocalypse, Doomsday and whatever you could come up with. It was going to happen at some point. I got there first."

Kara was deeply disturbed and knocked Alex out with one punch, "I'm so sorry." She whispered, before carrying her to a medical bay, "Dr Hamilton, examine her and call me when you get something."

J'onn walked in seconds later, "Kara, what is this?"

"Sir, there is something wrong with Alex. When I questioned her about the second missile, she was referring to aliens and humans in third person, like she was not one of us." J'onn frowned, "We will monitor her and do a shotgun so we can find out what has happened here."

Kara nodded before walking off.

* * *

 **A:N: And that's part 10! Thank you! So, what is going on with Alex? I honestly had the idea while I was just writing this chapter. I hope you enjoyed it!**


	11. Alert

"Scans are clear." Dr Hamilton confirmed. The digital clock above them read '17:50' and Kara stood anxiously, looking at Alex who was conscious and had no recollection of the moments before Kara knocked her out. In truth, Alex was concerned but not so much to the extent where Kara was. Kara was biting her nails, she was so nervous, "What-what about bloods?"

"They came back normal." Hamilton confirmed, before turning to J'onn, "But, this could possibly get worse. It's a hidden thing...Or..." Hamilton then turned to Alex, "Deep down down, do you regret what happened here? Does it bother you that you almost wiped out the entire planet?"

Alex shrugged, "I did what I had to do. I got what I wanted. I didn't care about casualties."

"Please tell me she is sane." Kara muttered, earning herself a glare from Alex, "What?! You don't just decide you hate all life overnight!"

"It depends on what sort of day you were having at the time. In my case, it was an awful day. And yes, awful enough for me to...end life on earth." Alex said the last part quietly. Kara frowned, "You don't remember telling Winn to set off the second missile do you?" Alex merely looked at her, before hesitating. J'onn frowned, "Alex?"

Alex stared at her feet, not knowing where to look, "I remember feeling like...Like, there was this deep, deep hatred inside of me. Like...Like everything I have ever felt bad about or felt...It just came to the surface and I felt unstoppable." She finally locked eyes with Kara, "Like...Like the red Kryptonite effect, but how can that be? I'm human, how would that work?"

"Or you were just extremely angry and you had to let it all go?" J'onn frowned.

"The hybrid." Kara gasped, "What if Lena isn't the only one? What if there was something in those missiles that CADMAS put there?"

"We'd know. Those missiles had sensors, so if anyone went near them, we'd know."

"Guys." Winn interrupted at the door, "Um, Miss Grant is here...She managed to walk here, like, she walked through the toxic air. I knew that she was invincible, just not literally."

Alex looked up at Kara, "Maybe they did get to the missiles, but that doesn't explain why she is creating hybrids...why destroy everything just to create her own aliens?"

Kara shrugged, and went straight to Lena.

* * *

"Humanity isn't human anymore, they can breathe the air outside. Miss Grant walked here, this plan has to be bigger Lena. Do you know anything else?"Kara said as she walked over to her in the lab.

"Nah, she wouldn't just destroy everything just to create more aliens, that would be stupid. What does sound right is that the intelligent ones survive so they can...I don't know, create bigger bombs to send across the universe to wipe out alien threat?" Lena said, clearly being careful with her wording, as she was finishing the last of the boxes. She then hissed, "No, this is way bigger than anything I have ever seen her try, but you also said that Alex was under the influence."

"The red Kryptonite effect." Kara replied, earning a laugh from Lena, "The what?"

"When she was under that influence, there was something more to it. Yes everything came to the surface but I saw something in her eyes Lena, something...Not of this world."

"But the red K made you bad and hot- I mean, I only saw what I did on the news and it was extraordinary...Hey, have you tried consulting Lord industries?"

"Even that's gone now." Kara shrugged, "But wait, Lord used a comatosed patient, or at least I think he did and he created a mirror of me. What if there are two Alex's?"

"No." Lena said sternly, "I'm thinking outside of the box." She then put her tools down and walked over to her, "What if there are two Maggie's?"

"What are you saying?"

"I'm saying that, I believe the real Maggie is still alive, and this is all just the beginning of something even bigger."

"Like what?" Kara asked, with her lip trembling. Lena walked so close to her, that their noses were almost touching, "What if there is a mole inside the DEO? One that is infiltrating as we speak?" She asked, close to a whisper. Kara was getting nervous, "Lena...You're scaring me."

"What if, what is happening to Alex, the possession and the dire thoughts...and poor old Maggie." Her tone suddenly changed, it was cold and calculated. Kara however was too slow to react to anything that was going on. Lena suddenly yanked her hair back, and held a shard of Kryptonite to her throat, "You move Supergirl and I will cut you in two." She sneered.

"You're not Lena." Kara gasped, swallowing the lump in her throat. There was a sharp laugh from Lena, "And Cat isn't who you think either." Kara panicked, "CADMAS, they...they can't have this power." She gasped, "What is going on?"

"You have to watch the fireworks Kara Danvers." She laughed, as red lights and alerts ran through the DEO.

* * *

"Mr Schott, what have you done?!" J'onn growled.

"I didn't!" Winn gasped, in a panic, "All of the missiles we had, they're activating." J'onn looked up at the screen, but then noticed that Cat had vanished, "Sir, we have a problem." J'onn turned around and saw the spot where Cat was stood, was now empty.

"Lockdown. Lockdown everything. Override, do whatever."

* * *

"The chimps are running around like mad." Cat chuckled as she walked into the science lab. Kara was only semi-conscious, and covered in her own blood. Cat frowned, "Does she know the truth yet?"

"Not yet." Lena confirmed.

"Your friends are still alive. Maggie, Lena and Cat, we just had to take their form to be able to infiltrate this stupid place and your sister? She is full of so much hate. She would be worthy of project CADMAS."

Kara tried to sit up but only got pushed back, "You leave my sister alone-"

"She basically ended the world...it's up to you to save it. But look at you, tied up, and bleeding. How low could you get Supergirl?"

"The hybrid, what is it? If Lena hasn't been...Lena this whole time. What the hell is it?!" Kara gasped.

Lena leaned over and injected Kara with Kryptonite, and as she did, Kara screamed so hard, that even Alex jumped to her feet and ran through the DEO herself.

Cat kept hold of Kara as she finally fell unconscious, "You'll find out very soon." She smiled.

* * *

As Alex reached the lab, she saw Kara and Lena were gone. Panic surged through her body and she didn't know what to do. Everything was going so fast. She looked over to the tables and saw the metal boxes full of anti-toxins were gone, "Crap." She muttered before running off again. The only thing left in the room was blood and Kryptonite, dripping from the edge of the table.


	12. Getting Back

It was cold. Kara was freezing. What was this? What was going on?

Dripping of water.

She thought she could hear it.

Blood, dripping from parts of her body.

She took a deep breath and exhaled.

She then heard feet.

Then a chain.

She was limp.

Her mouth was dry.

She couldn't see.

She was then blinded as the darkness that consumed her suddenly vanished.

"Wakey, wakey." She heard a soft, but dry voice say to her. As she managed to regain her full sight, she remembered that she had no powers. As she sat up and looked across the room, she saw none other than Maggie Sawyer and the former CEO of L-Corp. "L..." Her wording was dry. She couldn't form a word. She then looked up and saw none other than Lilian Luthor, "You survived." She said question involved, she knew it. She knew that Lilian had something to do with what was going on.

Kara had not yet noticed the various wires and I.V that were connected to her, injecting what looked like two different forms of a liquid. It was only once the nausea subsided that she took in everything that was happening. Then everything came crashing back down to earth.

Unknown strength now surged through her body, that was adrenaline, and Kara had no escape no matter how hard she pulled on the chains, "Let us go, Luthor. Or Spare them and take me!"

Lilian merely laughed, "And that would be so easy. Maggie would just head back to the DEO and my daughter would betray me. I think you'd better rethink your options Kara."

"Cut the crap Luthor." Maggie hissed.

Kara felt some joy that they hadn't changed Maggie in such a way her personality changed.

"You made my fiancee destroy the world, and you know that she would do anything for me-" Lilian then cut her off as she turned around, "Yes, but what you didn't know is that she thinks you are dead."

"What?!" Maggie spat.

Lilian smirked as she walked over, "We put you into a coma, created a doppelganger and sent you off to kill Supergirl, only your unconscious mind was too strong and our duplicate betrayed us. We had to kill her. And I think you'll find that's the only reason why you are still awake."

Maggie was speechless, and tears formed in her eyes. As Kara looked at her, she saw all of her hope was suddenly gone, "No Maggie, you cannot lose your hope, that is what they want. She hasn't moved on. Listen to me."

"She destroyed the world to avenge me. I'm alive while thousands are dead! Kara how am I meant to feel about that? I feel so _guilty!_ " Maggie snapped as tears now fell from her eyes and were cascading down her cheeks, she then glared at Kara, "WHY DIDN'T YOU OR J'ONN STOP HER?!"

Kara's heart fell in her chest.

"KARA!" Maggie shouted. Lena looked between them both and did not know what to say or do, "Kara." Lena interrupted, "Why didn't you, or Superman do anything?"

Kara shrugged, "J'onn was reminded of the slaughter of Mars and Kal and I were reminded of Krypton. We all heard the screaming and it made us stop. We couldn't do anything because we were haunted by memories of long ago." Kara now had tears in her eyes, and one found it's way down her cheek, "The truth is, after all of these years and of all the tolerance we once had..." She then took a breath, "All of us on that day, you wanna know what happened? We lost faith in humanity. We lost faith in humanity. You are as vile as each other. No matter how kind, good and gentle of a person you are...Humans have something dark within them that aliens ourselves cannot see. I lost my faith in Alex that day, and that hurts Maggie. She should rot in jail, but because she is my sister..." She then paused, "I don't know what to see or think of her anymore."

"Or maybe that's the power of what humans call, _love."_ Lilian intervened.

"No one destroys a whole planet out of love." Lena spat, "Kara, you love me right? As A friend? What would you do if I died?"

"Lena..." Kara said with her voice trembling.

"Tell me, what would you do?"

"She's an alien. There is a difference as to what she thinks and feels." Lilian interrupted.

"Oh shut up mother." Lena hissed, "You don't know what love is because you've never felt it."

Kara looked into Lena's eyes for a few moments, "You mean everything to me Lena. You are my only friend left. All I have is family. Maggie, Winn, J'onn..."

Maggie frowned, "What about Eliza and Jeremiah?"

"They died." Kara hissed.

There was then a moment of silence. Followed by a hissing noise. The four women in the room looked toward the sound. Cyborg Superman emerged from the darkness, "Is the hybrid ready?" He asked Lilian, glaring at the other three women.

"Almost." Lilian smirked.

Kara frowned, confusion swept over her face. "The hybrid? What is the Hybrid?"

Darkness then consumed the room, and there was nothing but silence.

* * *

 _PLANET DESTRUCTION IN THIRTY MINUTES._

 _PLANET DESTRUCTION IN THIRTY MINUTES._

 _T_ he sound ran through the DEO. Winn looked at Alex for help, but with no Supergirl around, no one could help them. Winn forced the lump in his throat down as he swallowed, "So this is your last act is it?" He hissed at Alex.

"There isn't another way. There is no way to clean the air. The earth isn't habitable and the longer we leave it, the more will die." Alex snapped.

"Oh I hope you rot in prison." He sneered.

Alex turned to him, glaring, "You think I wanted this? It's over, Winn. The sooner we accept our fate, the better."

"Whatever this hybrid is, it could save the world. You just decided to activate EVERY SINGLE MISSILE ON EARTH WHEN THERE COULD BE A CHANCE! YOU WANNA KNOW WHY J'ONN AND KARA GAVE UP ON YOU?!"

"Go on Winn, tell me!" Alex snapped, now merely inches from his face. Winn swallowed hard, and took a breath, "Because the one thing that normally makes a human happy destroyed you. Love destroyed you. If Maggie were here, she'd hate you for this and you know I'm right." His voice trembled as he spoke. Alex was forced to face reality. When she didn't reply, Winn knew she finally listened, "Switch off the detonation." He demanded.

"No." Alex sneered.

"AGENT DANVERS, AS OF NOW I AM STRIPPING YOU OF YOUR RIGHTS AS AN AGENT!" Winn shouted.

"Excuse me?" She spat, "You don't give me orders. Only J'onn does."

"He talked to me earlier, he stepped down because he couldn't bare to look at your stupid face any longer. I am your commander in-chief." Winn said bravely, "J'onn now believes that the humans got what they wanted. To reign supreme, and I don't want him to be proven right with our destruction. Call. It. Off." He ordered.

Alex glared at him for a second longer before calling out the order, "By the way Winn, J'onn would never ask you to do that. It was a load of crap wasn't it?"

"Yes, yes it was but..."

"Nice try." She sneered, before walking off.

Winn sighed in relief before the screens were hacked and none other than Lilian Luthor appeared, "Hello, remaining earthlings." She smirked, "How nice is it to be proven right? That all aliens are just evil? I have something special for you, a little project I have been working on. Oh agent Danvers." She said as she was walking away, "I have something that belongs to you."

"Supergirl." Alex breathed in shock, "What have you done to her?!"

"Well, if you insist. The hybrid needed a kickstart, so I have modified both her and Lena's DNA. Kara is still a boring old Kryptonian but Lena, oh she is so much more." She laughed, "But I wasn't on about Supergirl." She said with a sly tone, before showing a live image of Maggie. Alex's heart fell, "No, she can't be." She gasped in disbelief, "I DESTROYED THE WORLD BECAUSE I THOUGHT SHE WAS DEAD!" She screamed.

"You royally screwed up Danvers." Maggie said with a small smile, "But it's great to hear your voice."

Alex tried to smile,but found it too painful. Living with a heavy burden wasn't much to smile about.

"So the hybrid." Winn interrupted, "It's what we thought all along? Lena is the hybrid? Why all of this for just that?"

"Seeing how far someone will go for someone they love is always fun Mr Shott, but our hybrid...A double of Supergirl, yes."

Winn's face dropped, when he saw Lena right behind Lillian.

Lillian turned around, and as she did, Lena grabbed her and pinned her to a wall across the room, "This ends here." She sneered.

"No dear, it only end when I say it does." She smirked, "You won't kill me, we know you won't."

Lena looked over at Kara who appeared limp and lifeless, before glaring back at her mother who was now practically fighting for her life, "You got your prize, seeing how far a woman would go for someone she loved and your ultimate weapon. You made a huge mistake." She laughed darkly, "I'm sentient and I have a mind of my own which means, I can do this." She sneered before breaking her neck.

* * *

Alex and Winn gasped in surprise at the screen. Winn immediately got set on tracking them down, "Lena, I need coordinates."

"It's not safe for them to walk out there." Lena reminded him.

"I know, but you created five boxes."

"The anti-toxins, I know. I managed to manipulate the doppleganger into thinking like me. I will send you their codes over and put them on the land. Give it an hour for National City and another 24 for the globe. Oh and Winn, some of this destruction. It's not real. I can deactivate it."

"What? Some of it was like a perception filter?"

"Twenty percent was exaggerated. That bomb wasn't harmful enough."

"What do you mean it wasn't?" Winn gasped, "It was nuclear."

"A lot of the city was destroyed and lots of people died..."

"They did." Was all Lena said. The line then went dead. Lena rushed over to Maggie, "You'll be home soon. I promise."

* * *

 **A:N: This chapter wasn't as good as it could be, but I wrote it while tired, please tell me what you think and thank you all for reading and reviewing :)**


	13. The Truth and Nothing but The Truth

**A:N: This is a point of view chapter. It is from Winn's point of view at the start, but then dives in and out of each character while cutting in and out of the action, I hope it works :)**

* * *

 **WINN**

 _"She believes she's right, what she did in her mind was right. How in anyone's mind can she justify what she did? I get it, she lost Maggie, but Maggie is alive and still she shows no remorse for what she did. I mean, I feel guilty because I was the one who inputted the codes, I pressed that shiny red button. I could have said no, but she would have put a bullet through my head if I refused._ Winn was typing away at his computer, "Agent Danvers, they have another 15 minutes before they can start coming back. You cannot go out there!" Alex was busy getting kitted up, and she even had her gun fixed to her hip.

"Winn, I'm getting her back and then I'm getting my damn answers!" Alex snapped, clearly not wanting to listen.

 _"There she goes again. Damn I can't wait until she get's what she deserves, but then I wouldn't forgive myself if she was in prison for the rest of her life...Oh, what the hell?"_ Winn connected the video again, as he managed to find another signal, "Lena, hey. You have at least fifteen minutes before anyone can go out there."

"We also have another problem." Lena said to him, "It's Kara." Winn's eyebrows raised, "What about Kara?" Lena walked over to her and looked her over. Blue and red glows were coming through her skin, "She's...she's changing."

Alex then ran over to the screen, terrified, "Changing? Changing how? Is she awake? Lena, tell me what the hell is happening?!" Alex snapped. Lena appeared seconds later, "Winn, we can't accelerate the anti-toxin process, but Kara is ill. What mom gave her it's- it's rewriting her DNA on a molecular scale. I've no idea what she is turning into."

"Human." Maggie said from across the room, "That's the only thing it's gotta be. If your mom wanted you to be Supergirl, why not steal The Girl Of Steel's powers? It's like she switched the roles. You be the hero and she be the ordinary human. Lilian knows Kara would hate not being able to be who she really is. The only way to kill Supergirl would be taking away who she really is."

 _"Great, just what we need. A Luthor being the hero."_ Winn thought to himself, _"Wait a second."_ Winn then looked at Alex, "Alex..."

"This will destroy her." Alex sneered through gritted teeth, "This will end her!"

"ALEX!" Winn snapped, "We have thirteen minutes now and then Kara will be home, you just need to calm down."

* * *

 **LENA**

 _"I can't wait until all of this is all over. I am so sick and tired of it! This was the last straw. I have my best friend's powers, and now she will probably hate me. This is what comes with being a Luthor."_ Lena was cradling Kara in her arms. It had been five minutes since she last spoke to Winn. Kara began to stir. Lena heard her groan in her arms, "Hey." Lena smiled slightly, "You found me and now look how the tables turned." She laughed. Kara tried to crack a smile, "I like your eyes." They both laughed for a minute.

 _"God, she is so beautiful, when I looked into her blue eyes I felt so safe and now she is looking into mine, I wonder what she thinks now she is looking into mine."_

"What happened?" Kara mumbled.

"You fell unconscious, but don't worry, we've got you now. Ten minutes from now, we'll be at the DEO, home and dry."

Kara frowned, "You use that expression?"

"Yeah." Lena laughed, "Is that an issue?"

"No, it's kinda cute." She said with a smile.

"From what I can hear." Alex said, shifting her feet, "She's okay."

 _"She has a nerve. Blew up the planet and now she has the guts to use that tone with me. God, wait until I get my hands around her-"_ Lena's thoughts were cut short by Maggie looking at the DNA scans, "Yeah, no Kryptonian cells left." Kara then suddenly sat up, "What are you talking about?"

"Kara-" Lena began, "Um, to create the hybrid..." She took a breath, "Lilian extracted every single Kryptonian cell and put them inside of me...so I guess that makes you..."

"I'm human." Kara gasped. She found her throat had constricted, "No, No, that can't be right. You can't be me!"

"Kara-I'm..."

Kara got up and stumbled across to the computer, "Winn please tell me there is a way to reverse this."

 _"Now she hates me."_ Lena thought to herself, looking over at Kara. She saw how desperate she was. When she collapsed to her knees, Lena was instantly by her side, "Kara I'm so so sorry." Lena gasped.

"LET GO OF ME!" Kara snapped in tears, but Lena kept a firm grip on her. She soothed her and looked up at Maggie, who seemed only saddened by what was going on.

* * *

 **MAGGIE**

 _"I've messed up everything. Alex thinks I hate aliens and I think she is trying to forgive me. She can't though. She won't even be able to forgive herself for destroying the planet...I know the truth and none of them have a clue, yes Lena is the hybrid but...With Lena thinking that some of this was faked, she is so wrong."_ Maggie was looking down at both Lena and Kara, and seeing Kara hurting so much, hurt her too. She took a deep breath, leaning against a table. "Lena, there are some things you should know." She then stood straight and walked into an empty space in the room, "You all need to know that...I don't hate aliens...I was a cop at the time...I was young, arrogant and I thought I knew best...I'm sorry to all of you. None of you have a clue." She laughed half-heartedly, feeling a lump rise in her throat, "Lena, you think some of this was faked, but it wasn't. I knew what was gonna happen...Lilian knew you'd kill her and she knew some would survive...I knew everything that was going to happen."

Back at the DEO, everyone was listening, no one was stirring. Alex was holding back tears herself.

"Everything...I knew it would happen. Alex, you were meant to deploy a missile and for a few hours after you'd been out on duty, you set off that second missile. The reason you don't remember is because Lilian used your DNA and managed to do something to it to control you. I knew all about everything. Believe me, I didn't want anyone to get hurt...but I had to go along with it all. Alex isn't the guilty one here J'onn, I am." Maggie went quiet and just waited for a response from at least someone. But no.

Silence.

Alex tried to stop her lip from trembling, "How the hell can I forgive you after all of this? How would you know if I would use a stupid missile?"

Maggie held back tears, while shrugging, "It's the power of love."

 _Click._

The sound echoed through the warehouse, and as Winn looked at the screen, his jaw dropped, "Supergirl, what are you doing?" He gasped. Maggie turned around and there Kara was with a gun in her hand, "Little Danvers."

"Don't call me that, you don't _get_ to call me that _ever!"_ Kara sneered, forcing back tears, "You took away not only human life, but aliens too. You then took away what made me! Why didn't you warn ANY OF US?!"

"How could I? One word, and she would have killed you."

"Oh how heroic of you!" Kara sneered with sarcasm in her tone, "I'd rather die than listen to and see what I did on that day! You destroyed everything! You need to pay for what you did."

"Supergirl, no." Winn urged, "This isn't how this works."

"She destroyed everything." Kara sneered at Maggie. Lena was stood behind Kara, eyeing Maggie carefully, "Kara, this isn't the way and you know it isn't. Just put the gun down." She said softly, "Winn, how long before we can leave?"

"Five minutes." Winn confirmed.

"Come on Kara, five minutes and then you can go home to Alex...You miss her, I can tell."

"I just want life the way it was. I want normality and I can't have it because I don't have my powers."

Maggie sighed, "Just do it Kara."

"Don't you dare!" Lena sneered, "You don't get an easy way out Sawyer, that is not happening." The moment Lena turned around, the gun was fired.

"Just so you can't run anywhere." Kara sneered, looking at the blood now seeping from her leg. She then walked over to her and knelt in front of her, "You will answer for what you did, and no, Alex does not escape punishment so easily, but what she does do is have me...She will always have me." She sneered, before throwing the gun across the room.

Lena hugged Kara after she walked over, and only stared at Maggie on the floor, "It'll be okay Kara, the DEO will figure out what to do. I promise." Kara stayed quiet as tears were still in her eyes.

A few minutes later, an alarm bleeped. Winn looked over National City and surrounding areas, "The air is clean and ooh would you look at that, it's a nice sunny day."

"Come on Sawyer." Lena sneered as she walked over to her. She then looked at Kara, "You'll be alright here, won't you? While I take her to the DEO." Kara merely shook her head, "Yeah, I'll be fine." Lena looked at her with concern, but she picked Maggie up and flew her back to the DEO.


	14. Locking up

"Here she is." Lena sighed softly as she put Kara back on solid ground in the DEO. Alex rushed over and held her tightly. Kara was very unsure about weather to hug her back or not, so she stood there awkwardly until Alex pulled back. She then fixed her glasses on her face and cleared her throat, "I uh, I need to see Dr Hamilton about my gashes and I also need to get freshened up."

Alex almost jumped at the opportunity to help Kara out, "I can help, if you want." Alex said quickly. Kara looked down and then back up, not wanting to look at Alex, "No, no, I think you've done enough." She sighed, before walking off. Both Alex and Lena watched in despair as Kara headed to the medical bay. Lena forced herself to tear her eyes away from the now fragile blonde, "Director Henshaw, what will be happening will Sawyer from now on?"

Hank eyed the Luthor carefully, "I'm thinking more about Kara at this stage in time."

"Of course." She agreed with a slight nod. Hank then took a shallow breath, "But we have to find a way to give Kara her powers back."

"Sir, if we try, we could kill her."

"We?" Hank almost hissed, before walking away.

"Director..." Lena said, following him, "You can't trust me because I'm a Luthor, I get it- but Danvers gave the order to murder millions of people while I was trying to save everything."

Henshaw turned to Alex, "You should go and check on Kara." Alex merely nodded and went to check on Kara. Hank stopped Lena from following, "I didn't want to talk in front of Alex." He sighed, "Kara and I left earth after it's destruction because we were ashamed of Alex, I even thought of her as my own...But once I saw what she was truly capable of...I abandoned her. I should have her detained but I don't want to. It's not that I don't trust you...it's that I don't trust anyone now."

"I understand, however I do believe that both Alex and Maggie should recieve the same punishment...returning the planet to it's former glory, but I'm sure both Winn and I could collaborate and change what has been destroyed...Instead of it taking thousands of years, we can get it right in just months."

"That sounds impossible." Hank said with disbelief.

"Sir, I do have Kara's powers and while I believe that I shouldn't have them, Kara would still put them to good use."

"Indeed, however if you and Mr Schott are to change the world as you believe you can, you need to get to work."

"Of course." Lena said with a small smile, "Thank you sir." She said before walking off.

* * *

"Alex...I don't want to see you, I just want rest. Can you give me that?" Kara spat as she walked through the door. Alex closed the door and sat beside Kara who was laying down in the med bay, wearing nothing on her chest and bandages were draped over the once gaping wounds. Kara huffed out a sigh as Alex sat beside her. "I'm glad to see you back."

"Go outside Alex." Kara sneered.

"What?" Alex gasped with a confused smile. "Outside?"

"Up there...on the earth's surface. Stand out there and take a damned good luck at what you did!" Kara snapped, now forcing back tears, "You are worse than any alien I have ever met. _You_ destroyed everything I ever cared about without a second thought! I can _never_ forgive you Alex. To top it off, I have lost all of my powers! Oh you and Maggie are made for each other!" She sneered sarcastically.

"Kara stop please." Alex pleaded, taking her hand. Kara instantly yanked it back, and still refused to look at her bigger sister, "Get out of my life. You are _nothing_ to me. I used to look up to you. I loved you so much!" She now struggled to breathe as tears streamed down the sides of her cheeks. Nothing hurt Alex more than seeing Kara like this and it was only now that she began to regret ever giving the orders to destroy earth, "Kara I am so so sorry." She gasped, now in tears herself, shaking and struggling to keep herself together, "I will make this right. I promise you, I swear."

"NOTHING CAN MAKE THIS RIGHT, NOTHING YOU DO WILL MAKE THIS RIGHT!" Kara screamed, "GET OUT ALEX! GO! GET OUT OF MY LIFE! I NEVER WANT TO SEE YOU AGAIN! JUST GO!" Alex took the hint, and only merely nodded. She stood up and left the room in tears. As she walked down the corridor she wiped her tears away. Guilt finally took a hold of her and it was ugly to see.

"Agent Danvers, Miss Sawyer wants to see you." Another agent said from behind her. Alex cleared her throat, "I'll go and see her now."

* * *

"Danvers." Maggie said with nothing but a sigh, "Luthor and Winn will save the world. Once they do, you and I are going to jail for a long time."

"Why?"

"Why?" She gasped in disbelief, "Have you walked outside yet?"

"No, I meant...why did you use me? Why did you never tell me? Did you never trust me?"

"J'onn can read your mind too. If I told you-"

"It could have been stopped!"

"No, it was all planned, I had to stick to it, like a script."

"We are over. I hope you burn in hell!" Alex sneered and left the room. Maggie only went and sat back down. She stared at the wall and forced back tears as she removed her engagement ring. She then put it down on the bench and considered taking her own life as she sat there in the silence. She had to manipulate someone and she knew exactly _who_ to get to.

* * *

"Agent Danvers, it is with great regret that..." Henshaw began as he walked behind her. As Alex turned to face him, two agents stood behind her. Alex felt the hairs on her neck stand up and she instantly brought the two men down. J'onn laughed earnestly, "I knew you'd fight back."

"J'onn, this isn't the way, you know it isn't." Alex snapped.

"You killed millions Alex, you know I can't help you. For once, I don't want to help you."

"So what? You're gonna wipe my memory?"

"No, that's the coward way out. Both you and Sawyer will spend the rest of your lives behind bars. Without parole."

"J'onn please." Alex begged, as she was handcuffed.

"I saw my people die at the hands of White Martians, and then I saw aliens and humans alike, dying at your hands. No Alex."

Alex struggled as she was taken away, "J'onn, no!"

* * *

"You called?" Kara said as she walked into Maggie's cell later on, "Oh and, just in case you wanted to know, Alex has been arrested and she will be in jail for the rest of her life and the same for you. I should have killed you, but then if I did...You would get what you want."

"Your other mother, Eliza. She only kept you for experimentation." Maggie said, making a false lie to try and get at Kara, but she wasn't having any of it. She laughed sarcastically, "Next joke. You're pathetic."

"Okay..." Maggie said, challenging her, "Your life without Alex, it will be so lonely. You want her gone now because you are pissed but now you are a mere mortal, you will live out the rest of your life without her. No game night, no catching up on _Game of Thrones_ or _The Night Of,_ those days are gone now. So what will happen when you eventually have a home. Imagine a life without Alex. Do it." Kara stood in complete silence and began imagining. No Potstickers, no more picking out outfits, no more being there when she needed her. What the hell would she do without her?

"What will you do when she is gone Kara? You think it will be so easy every day to just come home and find her not waiting with a pizza or potstickers for you..." In truth all of what Maggie was saying was true, and it hurt Maggie as she was even thinking about it.

"Stop it Maggie." Kara sneered.

"You won't be able to touch her hand ever again, or even hug her. No contact, the first time in your life you feel like an actual Alien because you will have no contact to her other than her voice. You will watch her grow old...and everything you had before will be gone."

Kara angrily stamped in the keys into the pad, and opened the door, "Tell me, what else I will be without. I dare you." She sneered, pinning her to the glass.

"You will be without Alex for the rest of your life. You will be a sad old lady and you hate the truth. Eventually, she will learn to blame her alien sister for stealing her life and do you know what will happen? CADMAS will be reborn through her and then there will be no stopping it. We will destroy everything you, Lena and Winn will have built." She said with a sneer.

"CADMAS are dead and gone." Kara sneered, taking a knife from her back pocket.

"For now." Maggie said with a smirk, that finally made Kara snap. Kara pinned her to the glass and stabbed her several times, and when she knew Maggie was close to death, she held her up with one hand, and sneered at her, "CADMAS will never rise again." Kara then walked off, leaving the cell as several guards walked in.

As Kara walked by Lena on her way to Alex's cell, she stopped her, "You just killed Maggie, what the hell are you doing?"

"I need to see my sister. CADMAS can't rise again, it won't."

"You're right, it won't. It will never rise again. Kara, if you kill Alex...this will just carry on and you will be just like them. Come on, help me and Winn out. Let's change the world." She smiled.

* * *

It had been ten years since Earth's destruction, and now Kara Zor-El flew freely across the blue sky. Human's and aliens alike were united and Kara was the happiest she had ever been. As for Alex, she was still in jail. She saw Kara twice every week and she was becoming a better person. Guilt hadn't killed her, but what it did was make her a better person. She publicly apologized for what she did and accepted her fate. By Kara's standards, she was her big sister, that never changed. One big change in Kara's life was being able to be herself again. It took at least seven years, but now there were three superheroes, one of the most unlikely ones being Miss-Mrs Luthor-Zor-El. Everything was happy and shining. Crime still happened but everyone learned from the biggest disaster ever and now no one would want anything to change.

* * *

"Miss Danvers." The guard said, giving her mail. Alex was confused as she sat up, _must be from Kara_ she thought. When she opened it, she pulled out a black piece of card that read, _Welcome to CADMAS._ Alext let out a gasp of disbelief as she read the bottom note, _You didn't think I was really dead, did you Alex?_ It was signed, _Lilian Luthor._ Alex dropped the card on the floor. The only person who truly knew what was going on was Maggie, but she was dead. Alex recalled only a few minutes later a conversation both her and Kara had 9 years ago. She remembered that Maggie told Kara that she would restart CADMAS. This whole time, she thought she said it to get to Kara, now she knew it was true.

She couldn't do anything.

She wouldn't join or even rebuild CADMAS, she would _never_ do that.

But did she have a choice?

Alex was now terrified, not knowing who to talk to.

She was alone.

* * *

 **A:N: I do not know weather this is the final chapter, tell me what you think. Should I do a sequel at all? Also for those of you that Like the TV show, _Torchwood,_ I'm planning on writing a Supergirl crossover. Thank you all for sticking by me throughout this very complex plot in a fic that was only meant to be four chapters. Thank you all :)**

 **Update: I am indeed going to do a sequel, thank you all for reading this fiction. The sequel will be titled, 'No Way Out' Thank you everyone for reading. The new one will be up soon.**


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